Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= TCDB::G3LHZ0 (288 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 112 bits (280), Expect = 1e-29 Identities = 76/265 (28%), Positives = 127/265 (47%), Gaps = 5/265 (1%) Query: 11 FLVLPVLLLVAFSAVIPLMTVVNYSVQDTFGNNEF--FWAGTDWFVQTLHSDRFWESLQR 68 +L +P LL + PL+ S+Q N + + G + + RFW L Sbjct: 7 WLTIPALLTITGVFAYPLLRAAWLSLQALNLNTQLQPVFIGLANYQRLWGDSRFWGDLFN 66 Query: 69 NLLFSFIILALEIPLGIFIALNMPKSGPGVPVCLVLMALPLLIPWNVVGTIWQVFGRVDI 128 +F+ ++LE+ LG+ IAL + + + LP ++P V+ W Sbjct: 67 TTVFTVTSVSLELVLGLAIALLLHQPSRWRGPLRTIALLPWVLPTAVMALGWAWIFNDPY 126 Query: 129 GLLGHTLEAIG---LDYNYVRDPIDAWVTVIVMDVWHWTSLVVLLCYAGLVSIPDAYYQA 185 G+ L+ +G N++ +P AW+T++ DVW T V +L AG +IP+ Y+A Sbjct: 127 GVWNDWLQQLGWIAAPINWLGNPRWAWLTLVAADVWKTTPFVAILLLAGRQAIPEDLYEA 186 Query: 186 AKIDGASRWSVFRYIQLPKMKRVLLIAVLLRFMDSFMIYTEPFVVTGGGPGNSTTFLSID 245 ++GA+ W F I LP ++ L IA+L R +F ++ V+TGGGP NST L++ Sbjct: 187 HCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGLFDLVKVMTGGGPANSTETLALY 246 Query: 246 LVKMAVGQFDLGPAAAMSIIYFLII 270 A+ D G A ++I+ I+ Sbjct: 247 AYTTALRYLDFGYGATLAIVTAAIL 271 Lambda K H 0.329 0.143 0.464 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 291 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 288 Length of database: 292 Length adjustment: 26 Effective length of query: 262 Effective length of database: 266 Effective search space: 69692 Effective search space used: 69692 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory